Pay for the chief executives of Washington’s largest public companies declined in 2012 compared to the year before, as compensation increasingly shifted to favor stocks over cash.

Among the 89 highest-paid chief executives, total compensation fell 4.52 percent in 2012. Median pay dipped 3 percent to $3.22 million from $3.32 million, according to a new survey conducted for Capital Business by Equilar, an executive compensation research firm. In some cases, the drop reflects the diminishing returns of local firms grappling with a pullback in government spending. A similar study Equilar did for the New York Times found that median pay rose 16 percent for the top 200 chief executives at public companies nationally with at least $1 billion in revenue.

The salary packages come as a financial reform known as “Say on Pay” enters its third year. The practice was established to give shareholders a non-binding vote on proposed compensation packages in an effort to curb surging CEO pay in the wake of a financial crisis that led to widespread bank bailouts and a deep recession.

The effect so far has been more a tapping on the brakes than any sudden halt. Shareholders at an overwhelming majority of companies nationwide — 92 percent, as of June — pass say-on-pay with more than 70 percent approval, according to data compiled by Semler Brossy Consulting Group in Los Angeles.

“If [Washington area] annual pay is slightly down, it could reflect concerns about say-on-pay. But that does not mean that pay is not any more tightly tied to performance than it was before, and I don’t see that changing any time soon,” said Nell Minow, an investor advocate and co-founder of the New York-based governance advisory firm GMI Ratings.

In the past year, companies say they have gone to greater lengths to define exactly how their executives are being paid, using benchmarks such as overall revenue, profits or share price to guide them.

At the top of the highest-paid list for the third year in a row: David M. Zaslav, president and chief executive of Discovery Communications, who received $49.93 million, including $8.33 million in cash and $41.17 million in stocks and options. Zaslav, who largely met goals for revenue, operating income and cash flow, nevertheless saw his pay fall 4.7 percent last year as the cable company reset his stock compensation. Discovery declined to comment.

Lisa A. Hook (No. 15), president and chief executive of Neustar, pulled in $7.23 million last year, making her the highest-paid woman on the list.

Among the 89 highest-paid chief executives in the area, stock options — which allow employees to buy a certain number of shares in the future at a price set now — were down 54.8 percent in 2012, according to data from Equilar. Salaries dropped 5.93 percent, and bonuses fell 13.01 percent. Meanwhile, components more-closely tied to a company’s track record — stock awards and performance incentives, for example — rose 75.86 percent and 6.02 percent, respectively.

“The headline this year is that companies are trying harder to explain their executive compensation programs to their largest institutional investors,” said Charlie Tharp, chief executive of the Center on Executive Compensation, a group established by an association of human resource directors. “There has been a continued trend toward stock awards and performance bonuses, and a decrease in options.”

That certainly was the case for Robert J. Stevens (No. 2), who retired as chief executive of Lockheed Martin at the end of 2012. More than one-third of Stevens’ $23.85 million came from $8.29 million in performance incentives. That signals a marked increase from the year before, when Stevens received $4.4 million, or 21 percent of his pay, in performance incentives.

Those figures are in line with national trends as shareholders call for more transparency in executive pay, said Christopher McGoldrick, a spokesman for Equilar.

“We’re seeing a lot of companies moving to pay their executives in performance shares — stocks that come with certain metrics that executives have to meet,” McGoldrick said. “It’s nice that the stock market is improving, but even aside from that, a lot of companies are moving toward stocks to show shareholders that they’re linking compensation to performance.”

At some area companies, executive pay closely mirrored the firm’s broader trajectory. Cardinal Financial chief executive Bernard H. Clineburg (No. 69), for example, received a 53 percent boost in pay to coincide with a 62 percent increase in profits.

At Washington Real Estate Investment Trust, both the company’s profits and the chief executive’s pay fell by more than 70 percent. George F. McKenzie (No. 76) was paid $1.06 million last year — down from $3.93 million the year before (when he was ranked 31) as the company’s annual profits fell to $23.71 million from $105.38 million in the same period.

Not all firms have managed to align pay with performance. David Schaeffer (No. 9), founder and chief executive of Cogent Communications, received $8.75 million last year — more than five-fold the $1.69 million he made in 2011 — even as the company posted a $4.25 million loss.

Schaeffer’s pay package was rejected by nearly 60 percent of the company’s shareholders in April, making it the second time the company failed say-on-pay. (The first came in 2011).

Cogent did not return calls seeking comment. The company explained Schaeffer’s pay package, which included $8.41 million in stock awards, in a proxy statement filed earlier this year.

“The method of compensation decision making employed by the company does not lend itself to extensive analytical and quantitative disclosure,” the company said. “Most of the analysis that goes into compensation determinations is simply the subjective business judgment of the company’s CEO and the board of directors.”

There is debate about exactly how much progress has been made in regulating executive pay, which has been under increased scrutiny since the economic downturn. The House of Representatives in June voted to repeal a proposed rule that would require companies to report the difference in pay between their chief executive and average worker.

“The gap between the average American and the highly paid is widening, so this issue becomes bigger and bigger,” said Alan M. Johnson, managing director of Johnson Associates, a compensation consulting firm. “What we’re seeing is that the reduction in perks continues. Excessive severance, excessive contracts, excessive retirement benefits have been scaled back significantly.”

Seventeen of the 89 highest-paid executives received bonuses last year, down from 27 the year before, reflecting a broader move away from discretionary payouts. Jay L. Johnson (No. 5), chairman and chief executive of General Dynamics, walked away with the second-biggest bonus, valued at $3.6 million — roughly 20 percent of his overall package.

Seven executives on this year’s list received more than double what they did the year before. Among them: Robert S. Silberman (No. 41) of Strayer Education, whose pay package increased 413 percent; Richard J. Hendrix of the investment firm FBR, up 241 percent; and Martine A. Rothblatt (No. 28), CEO of drugmaker United Therapeutics, up 185 percent.

In the coming year, analysts say they expect investors to continue to ask more questions about exactly how companies are quantifying an executive’s performance.

“The next frontier is looking at how stringent the goals actually are,” said McGoldrick of Equilar. “Rigor in performance metrics is certainly something that’s getting a lot more attention. It’s easy to pay executives based on metrics but if the bar isn’t set high and it’s something they can easily exceed, you’re really not tying compensation to the company’s performance.”